Hundreds of Khan's supporters protested in Karachi against the results, saying the election was "stolen" from his party, PTI.
Their candidates were forced to run as independents by electoral officials.
They won 93 seats out of 264, while their biggest rival, the party of another former prime minister, Nawaz Sharif, won 75.
That means the largest single party in parliament is Sharif's.
And the independents will lose out on reserved parliamentary seats that are given to the strongest parties.
"Today's demonstration is a protest against the forces that have stolen the people's mandate. This is a protest against those forces that do not accept public opinion and think they can impose their decisions on the public."
The PTI supporters also condemned the delay in publishing the final tally of votes.
That took place more than 60 hours after voting ended.
Pakistan's interim government said the voting count delay was caused by communications issues due to a mobile internet outage on election day.
Authorities said the outage was for security reasons, but it's drawn concern from human rights groups and foreign governments.
Coalition talks are now full steam ahead.
In the coming days, a prime ministerial candidate has to show a simple majority of 169 seats in the National Assembly when the house is called.
Khan-backed candidates will have to try and join a smaller party in parliament.
While Sharif's party said that he had met with representatives of the minority regional MQM party, who had agreed to "in principle work jointly in the larger interest of the country."
MQM supporters were celebrating in the early hours of Monday, after winning seats in the election.
An MQM leader confirmed the meeting, but said no formal coalition agreement had been made.
If no one is able to form a government, Pakistan's army, the most powerful and organized force in the country, could step in to restore order and take power - as it has done three times already in the country's 76-year history.
